Cancer diagnostics, therapeutics, and drug discovery associated with macropinocytosis

ABSTRACT

The present invention is directed to methods of inhibiting both proliferation and survival of cancer cells and for treating a subject having cancer. The present invention is further directed to methods of diagnosing cancer in a subject and identifying cancer therapeutics.

This application is a division of U.S. application Ser. No. 14/009,013,filed on Sep. 30, 2013, which is a national stage application under 35U.S.C. § 371 of PCT Application No. PCT/US2012/031828, filed Apr. 2,2012, which claims the priority benefit of U.S. Provisional PatentApplication Ser. No. 61/470,945, filed Apr. 1, 2011, which is herebyincorporated by reference in its entirety.

This invention was made with government support under 2R01CA055360-19A1awarded by the National Institutes of Health. The government has certainrights in the invention.

FIELD OF THE INVENTION

The present invention is directed to methods of diagnosing and treatingcancer in a subject. A high-throughput method of identifying compoundssuitable for treating a subject having cancer is also disclosed.

BACKGROUND OF THE INVENTION

Oncogenic mutations in Ras-encoding genes are found in approximately 30%of all tumors and are most prevalent in carcinomas of the pancreas,colon, lung and bladder. These mutations have profound effects onproliferation, cell survival and tumor invasion. Ras orchestrates theseevents by activating downstream effector pathways that regulate actinreorganization, gene expression and macropinocytosis.

Macropinocytosis is a stimulated form of fluid-phase uptake thatinvolves extensive plasma membrane remodeling and the internalization ofextracellular fluid via large endocytic structures calledmacropinosomes. Macropinocytosis plays a key role in various biologicalprocesses, including immune surveillance, nutrient uptake and pathogeninfection. Interestingly, macropinocytosis is also stimulated in cellsharboring oncogenic mutations; however, the functional significance ofthis stimulation is unknown.

The present invention is directed to overcoming these and otherdeficiencies in the art.

SUMMARY OF THE INVENTION

A first aspect of the present invention is directed to a method ofinhibiting cancer cell proliferation and/or cancer cell survival. Thismethod involves selecting cancer cells having enhanced macropinocytosisand administering to the selected cancer cells a macropinocytosisinhibitor under conditions effective to inhibit cancer cellproliferation and/or cell survival.

Another aspect of the present invention is directed to a method oftreating a subject having cancer. This method involves selecting asubject having cancer, wherein the cancer is characterized by cancercells having enhanced macropinocytosis and administering, to theselected subject, a macropinocytosis inhibitor under conditionseffective to inhibit cancer cell proliferation and/or survival in thesubject, thereby treating the subject having cancer.

Another aspect of the present invention is directed to a method ofdiagnosing cancer in a subject. This method involves administering tothe cells of a subject a macropinocytosis marker and detecting thepresence of the macropinocytosis marker in cells of the subject. Themethod further involves comparing the amount of macropinocytosis markerin cells of the subject to the amount of macropinocytosis marker innon-cancer cells and making a diagnosis of cancer in the subject basedon said comparing.

Another aspect of the present invention is directed to a high-throughputmethod of identifying a cancer therapeutic. This method involvesproviding a population of cells having enhanced macropinocytosis andproviding a macropinocytosis marker. The method further involvescontacting the population of cells with a candidate compound underconditions effective for the candidate compound to inhibitmacropinocytosis and detecting and comparing the uptake of themacropinocytosis marker in the presence and in the absence of thecandidate compound. A decrease in marker uptake in the presence of thecandidate compound compared to in the absence of the candidate compoundidentifies a cancer therapeutic

The identification of new therapeutic strategies that offer significantimprovement in clinical outcomes for oncogene-mediated cancers isurgently needed. Recent years have witnessed a renewed appreciation ofthe altered metabolic behavior of tumor cells and the critical role thatsuch metabolic reprogramming plays in conferring growth and survivaladvantages to tumor cells. Of particular relevance, is the now widelyaccepted notion that cancer cells display a heightened state ofdependency on glutamine, which they utilize as a substrate for variousmetabolic processes. The present invention defines a new mechanism thatcontrols glutamine supply in cancer cells, and as such, will advance ourunderstanding of the molecular pathways that account for the metabolicphenotype of oncogene-positive cancer cells. Furthermore, the presentinvention has identified new strategies for inhibiting cancer cellgrowth and survival via the targeting of tumor cell bioenergetics andmacropinocytosis.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1B show macropinocytosis in HeLa cells expressing oncogenicRas^(V12). FIG. 1A is a panel of fluorescent photomicrographs showingnuclear staining (DAPI), H-RAS^(V12) expression, and macropinocytosisuptake (Dextran) in HeLa cells. The bottom right image shows an overlayof the nuclear, H-RAS^(V12), and Dextran fluorescent localization. FIG.1B is a bar graph showing quantification of macropinocytosis in HeLacells as a function of H-RAS^(V12) expression.

FIGS. 2A-2C show macropinocytosis in NIH 3T3 cells transformed byoncogenic Ras^(V12). FIGS. 2A-2B are fluorescent photomicrographsshowing macropinocytotic uptake in untransformed cells (vector; FIG. 2A)and cells genetically modified to express K-ras^(V12) (FIG. 2B). FIG. 2Cshows the quantitation of macropinocytotic uptake in both the controland K-ras^(V12) cells.

FIGS. 3A-3E show macropinocytosis in bladder (FIGS. 3A-3B) andpancreatic cancer cells (FIGS. 3C-3D), harboring oncogenic ras mutations(FIGS. 3B, 3D, and 3E). Macropinocytosis in bladder and pancreatic cellshaving a non-mutant ras gene is shown in FIGS. 3A and 3C, respectively.

FIGS. 4A-4D are fluorescent photomicrographs shows macropinocytosis(Dextran) in CD45⁺ immune cells (FIGS. 4C-4D) recruited to pre-cancerouslesions in p48-Cre; LSL-KRasG12D mice. The sections shown in FIGS. 4Aand 4B are co-labeled with CK19, a marker of pancreatic duct cells andFITC-labeled dextran.

FIGS. 5A-5E show macropinocytosis in heterotopic xenograft tumorsderived from human MIA-PaCa-2 pancreatic cancer cells. For the xenograftmodel, 1×10⁶ pancreatic cancer cells (MIA-PaCa-2) were injectedsubcutaneously into the flanks of nude mice (FIG. 5A) andmacropinocytosis by the tumor cells was analyzed three weeks postinjection. To detect macropinocytosis, mice were intratumorally injectedwith fluorescently-labeled fluid-phase marker (FITC-dextran) at 2 mg/g.FIG. 5C shows macropinocytosis positive cells within the tumors. FIG. 5Bshows nuclear cell staining of the cells in FIG. 5C using DAPI. Todistinguish between transplanted and host immune/stromal cells, thesections were counterstained with an epithelial-specificanti-cytokeratin antibody (FIG. 5D). An overlay of DAPI, dextran andcytokeratin staining is shown in FIG. 5E.

FIGS. 6A-6B show protein uptake in HeLa cells expressing oncogenicRas^(V12). FIG. 6A is a panel of fluorescent photomicrographs showingnuclear cell staining (top, left), mutant H-Ras^(V12) expression (top,right), protein uptake (FITC-BSA; bottom, left), and co-localization ofthe three (bottom, right). FIG. 6B shows the quantitation of proteinuptake in oncogenic Ras^(V12) expressing cells

FIGS. 7A-7C show albumin internalization co-localizes withdextran-positive macropinosomes. FIGS. 7A and 7B show albumininternalization and macropinocytosis, respectively in HeLa cells.Internalization of albumin into macropinosomes is shown in the overlayimage of FIG. 7C.

FIGS. 8A-8B show that acidic cellular compartments are increased inoncogenic Ras^(V12)-expressing HeLa cells. FIG. 8A shows Lysotracker(Invitrogen) staining, which labels acidic compartments, in control HeLacells not expressing oncogenic H-Ras^(V12) (DOX) and HeLa cellsexpressing H-Ras^(V12) (NO DOX). FIG. 8B shows the quantitation ofLysotracker staining.

FIGS. 9A-9B demonstrate that macropinosome contents are destined for anacidic cellular compartment. The fate of the macropinosomes was followedvia pulse chase experiments and their fusion with lysosomes wasmonitored by co-staining with lysosomal markers (i.e., Lysotracker;FIGS. 9A and 9B left and right panels). Cells were pulsed withTMR-dextran (middle and right panels) and incubated withTMR-dextran-free media for 0-hours (FIG. 9A) and 6-hours (FIG. 9B)

FIGS. 10A-10B depict albumin catabolism in oncogenicRas^(V12)-expressing HeLa cells. Albumin degradation was measured via apulse-chase experiment consisting of incubating pancreatic cancer cellswith BSA and subsequently chasing with BSA-free media. The presence ofinternalized BSA was measured by immunostaining the cells with ananti-BSA antibody and a fluorescent secondary antibody (FIG. 10A). Thetop panel of FIG. 10A shows anti-BSA staining in the absence of chasingin BSA-free media (T=0) and the bottom of panel FIG. 10A showsBSA-staining after 3 hours of chase. The intensity the intensity of thefluorescent signal that was incorporated into vesicular spots wasquantified using automated spot detection (FIG. 10B).

FIGS. 11A-11B demonstrate that glutamine (FIG. 11A) and glutamate (FIG.11B) production in NIH 3T3 cells transformed by oncogenic K-Ras isincreased in the presence of physiological levels of albumin (i.e., 2%).

FIGS. 12A-12B show that oncogenic Ras-expressing HeLa cells have asurvival advantage when deprived of glutamine in the presence ofconventional albumin-containing medium. FIG. 12A shows the finelycontrolled expression of oncogenic H-Ras^(V12) in HeLa cells withdecreasing concentrations of tetracycline. FIG. 12B is a graph showingthe survival ratio of oncogenic Ras-expressing HeLa cells in thepresence of decreasing amounts of tetracycline correlating to increasinglevels of oncogene expression (50 ng/mL, 10 ng/mL, or 0 ng/mL oftetracycline) over 5 days.

FIG. 13 demonstrates that increasing the protein content of the media(0.4% or 2% albumin) enhances viability of oncogenicRas^(V12)-expressing HeLa cells.

FIGS. 14A-14B show that the survival advantage of oncogenicRas-expressing HeLa cells in glutamine-free media containing low BSA(FIG. 14A) or 2% BSA (FIG. 14B) is suppressed by EIPA, amacropinocytosis inhibitor.

FIG. 15 shows that extracellular BSA partially rescues K-Rastransformation-associated glutamine addiction in NIH 3T3 cells. Thegraph depicts cell viability over time.

FIGS. 16A-16D demonstrate BSA rescue of glutamine addiction in the T24bladder cancer (FIGS. 16A-16B) and MIA-PaCa-2 pancreatic cancer celllines (FIGS. 16C-16D) harboring oncogenic Ras mutations. FIGS. 16A and16C show rescue of cell viability with higher extracellular albuminconcentrations in the T24 and MIA-PaCa-2 cell lines, respectively. FIGS.16B and 16D plot the survival advantage (a ratio of the viability of thehigh protein media cells to the low protein media cells) for thetimepoints indicated.

FIGS. 17A-17B are graphs charting cell growth of K-Ras^(V12)-transformedNIH 3T3 cells and vector only controls in physiological (FIG. 17A) andsub-physiological levels (FIG. 17B) of glutamine.

FIGS. 18A-18B are graphs showing the effect of increasing proteincontent of the growth media on cell proliferation inK-Ras^(V12)-transformed NIH 3T3 cells (FIG. 18A) and control cells (FIG.18B) in sub-physiological glutamine conditions.

FIGS. 19A-19B demonstrate that extracellular BSA partially rescuesglutamine addiction selectively in T24 cells (FIG. 19A) harboring anoncogenic Ras mutation, and not 5637 cells (FIG. 19B) which have anon-mutant Ras gene.

FIGS. 20A-20C show the effects of albumin supplementation on cellgrowth. FIG. 20A shows intracellular levels of glutamate andα-ketoglutarate are elevated following the incubation of NIH 3T3[K-RasV¹²] cells in complete medium supplemented with 2% albumin(“CM+Alb”) compared to complete medium alone (“CM”). Intracellularaccumulation of both metabolites was blocked by 25 mM EIPA treatment(“CM+Alb+EIPA”). Data are expressed as arbitrary units and are presentedrelative to the values obtained for the CM condition. FIG. 20B showsthat the effects of EIPA treatment (25 mM) are suppressed by increasingthe glutamine levels in the growth media to the indicated concentrations(i.e., 0.5 Q indicates 0.5 mM glutamine) or the addition to the mediumof 7 mM dimethyl α-ketoglutarate (“KG”), a cell-penetrant form ofα-ketoglutarate. The concentrations of glutamine used represent theminimum concentration that is required to rescue the effects of EIPA foreach cell line. Data are presented relative to the values obtained forthe 0.2 Q+Alb condition. Error bars indicate mean +/− SEM for n=3independent experiments. Statistical significance was determined viat-test; *p<0.05, **p<0.01. FIG. 20C shows the analysis of DQ-BSAfluorescence in NIH 3T3 [K-Ras^(V12)] cells that were co-incubated withDQ-BSA (green) and TMR-dextran (red) and fixed either immediately at theend of the incubation (T=0) or following a 1 hour chase in media free ofboth DQ-BSA and TMR-dextran (T=1 HOUR). The fluorescent signal emanatingfrom DQ-BSA (T=1 HOUR) is an indication of albumin degradation. Insetsrepresent a higher magnification of the boxed area. Images shown in arerepresentative of at least 3 independent experiments.

FIGS. 21A-21B show the high-throughput quantification ofmacropinocytosis in HeLa cells expressing Oncogenic Ras^(V12).

FIGS. 22A-22B show the dose-response analyses for the macropinocytosisinhibitors LY294002 (FIG. 22A) and EIPA (FIG. 22B) using thehigh-throughput compatible macropinocytosis assay in oncogenicRas^(V12)-expressing HeLa cells.

DETAILED DESCRIPTION OF THE INVENTION

A first aspect of the present invention is directed to a method ofinhibiting cancer cell proliferation and/or cancer cell survival. Thismethod involves selecting cancer cells having enhanced macropinocytosisand administering to the selected cancer cells a macropinocytosisinhibitor under conditions effective to inhibit cancer cellproliferation and/or cell survival.

In accordance with this aspect of the present invention, the selectedcells have enhanced macropinocytosis that is stimulated or mediated bythe expression of an oncogene. Accordingly, a cell having enhancedmacropinocytosis includes any cell having an activated oncogene. As usedherein, “oncogene” is a gene that plays a normal role in the cell as aproto-oncogene, but has been altered by mutation and contributes to thegrowth of a tumor. Oncogenes are well known in the art and include,without limitation, c-Sis, epidermal growth factor receptor (EGFR),platelet-derived growth factor receptor (PDGFR), vascular endothelialgrowth factor receptor (VEGF), HER2/neu, Src-family of oncogenes,Syk-ZAP-70 family of tyrosine kinases, BTK family of tyrosine kinases,Abl, Raf kinase, cyclin-dependent kinases, Ras, myc, Wnt, and Trk. Inone embodiment of the present invention, the selected cell expresses aras oncogene, e.g., a mutant H-ras gene, mutant N-ras gene, or a mutantK-ras gene. In another embodiment of the invention, the selected cellexpresses a v-src or a mutant c-src gene. In another embodiment of theinvention, the selected cell expresses an oncogenic EGFR gene.

While oncogene-stimulated macropinocytosis has been previouslydemonstrated (see, e.g., Bar-Sagi et al., “Induction of MembraneRuffling and Fluid-Phase Pinocytosis in Quiescent Fibroblasts by RasProteins,” Science 233(4678):1061-68 (1986), which is herebyincorporated by reference in its entirety), the selective advantage thatenhanced macropinocytosis confers to the oncogenic cells has not beenappreciated. As described herein, applicants have found that oncogeniccancer cells gain a survival advantage, measured by their metabolicactivity, as a result of enhanced macropinocytosis. Enhancedmacropinocytosis in oncogenic cells results in the increasedinternalization of extracellular protein, which is used as a nutrientsource in cancer cells. The increased protein uptake in low glutamineconcentrations, which is typical of the in vivo cancer cell environment,enhances cancer cell viability. Accordingly, inhibiting macropinocytosisin oncogenic cancer cells inhibits proliferation and survival of thesecells, resulting in inhibition of tumor formation and growth.

In accordance with this aspect of the invention, a suitablemacropinocytosis inhibitor is any macropinocytosis inhibitor known inthe art. Suitable macropinocytosis inhibitors include, withoutlimitation, phosphatidylinositol (PI) 3-kinase inhibitors, Rho GTPaseinhibitors, actin polymerase inhibitors, PKC inhibitors, phospholipase Cinhibitors, Na⁺/H⁺ exchange inhibitors, and Erk/Mek/p38 combinationinhibitors.

Because of its strict requirement for actin, the most commonly usedinhibitors of macropinocytosis are actin polymerase inhibitors such ascytochalasins, particularly cytochalasin D. Macropinocytosis is alsohighly dependent on the activity of phosphatidylinositol (PI) 3-kinase(PI3K) and the activity of the Rho family small GTPases, which regulateactin rearrangements. Inhibitors of PI 3-kinases, such as wortmannin andLY294002, and Rho GTPases, such as toxin B, are suitable inhibitors ofmacropinocytosis for use in the present invention. In addition amilorideand its analogues (e.g., 5-N-ethyl-N-isoproamiloride (EIPA), dimethylamiloride (DMA)), which inhibit the Na⁺/H⁺ exchange, can also be used inthe methods of the present invention to inhibit macropinocytosis incells.

Several promising molecular approaches in targeting the process ofmacropinocytosis have emerged recently, which target ARF- and Rho-familyGTPases. Overexpression of ARF6 locked in its GTP-bound form,dominant-negative forms of the Rho family GTPases, and theautoinhibitory domain of the Rac-dependent kinase PAK1, all result in aninhibition of macropinocytosis.

Additional specific inhibitors of macropinocytosis that are suitable foruse in the methods of the present invention include, without limitation,2-nitro-4-carboxyphenyl N,N-diphenylcarbamate (NCDC),hexodecylphosphocholine (HPC), U73122, and Rottlerin.

In one embodiment of the present invention, inhibition of cancer cellproliferation and/or cancer cell survival is carried out ex vivo. In analternative embodiment of the invention, inhibition of cancer cellproliferation and/or survival is carried out in vivo.

In vivo inhibition of cancer cell proliferation and/or survival requirestargeted delivery of the macropinocytosis inhibitor to the oncogeniccells to achieve selective inhibition of macropinocytosis in only thesecells. Since macropinocytosis plays a key role in a number of biologicalprocesses, general or systemic inhibition of macropinocytosis isundesirable. Methods of targeting macropinocytosis inhibitor deliveryare described infra.

Another aspect of the present invention is directed to a method oftreating a subject having cancer. This method involves selecting asubject having cancer, wherein the cancer is characterized by cancercells having enhanced macropinocytosis. The method further involvesadministering to the selected subject, a macropinocytosis inhibitorunder conditions effective to inhibit cancer cell proliferation and/orsurvival in the subject, thereby treating the subject having cancer.

In accordance with this aspect of the present invention, a “subject” or“patient” includes any animal. Preferably, the subject is a mammal, morepreferably, the subject is a human.

Subjects suitable for treatment in accordance with this aspect of theinvention are those subjects having cancerous cells which exhibitenhanced macropinocytosis. Therefore, selecting a subject suitable fortreatment in accordance with this aspect of the present invention mayinvolve administering to cells of the subject a macropinocytosis marker,detecting the macropinocytosis marker in the cells of the subject, andcomparing the amount of macropinocytosis marker in the cells of thesubject compared to non-cancerous cells (e.g., non-cancerous cells ofthe subject). Methods of measuring the level of cellularmacropinocytosis in a subject are described in more detail infra.

In one embodiment of the invention, the enhanced macropinocytosis isstimulated or mediated by an oncogene as described supra. In otherwords, suitable subjects for treatment in accordance with the methods ofthe present invention, include those subjects having anoncogene-mediated cancer condition. Cancers that typically have anoncogene component include, without limitation, pancreatic cancer, lungcancer, breast cancer, ovarian cancer, colorectal cancer, thyroidcancer, liver cancer, bladder cancer and leukemia.

Any of the macropinocytosis inhibitors described supra can beadministered to the subject in accordance with this aspect of thepresent invention. In a preferred embodiment of the invention, themacropinocytosis inhibitor is targeted to cancer cells, therebyinhibiting macropinocytosis in cancer cells, but not in normal,non-cancerous cells. As noted above, systemic or general inhibition ofmacropinocytosis in an individual is not desired. To achieve selectiveinhibition of macropinocytosis in cancer cells only, the agent isadministered directly to the site of the cancer cells (i.e., directtumor injection). Alternatively, the macropinocytosis inhibitor ishoused in a targeted delivery vehicle (suitable delivery vehicles aredescribed infra). In yet another embodiment, selective targeting of themacropinocytosis inhibitor is achieved by coupling the inhibitor to atargeting ligand for directed delivery of the inhibitor.

In accordance with this aspect of the invention, ligand directeddelivery of the inhibitor is achieved using a cancer cell specificligand targeting strategy. Suitable ligand directed cancer celltargeting systems are known in the art and include, without limitation,Eph-ligand based delivery (see U.S. Patent Publication No. 2010/0240594to Pellecchia et al., which is hereby incorporated by reference in itsentirety), vasoactive intestinal peptide, somatostatin, gastrinreleasing peptide, bombesin, or substance P ligand based deliverysystems (see U.S. Patent Publication No. 2010/0184651 to Maithal et al.,which is hereby incorporated by reference in its entirety), urokinase,urokinase A chain, epidermal growth factor (EGF), transforming growthfactor-alpha (TGFα), insulin-like growth factor, interleukin-4 (IL-4),interleukin-6 (IL-6), platelet-derived growth factor (PDGF), fibroblastgrowth factor (FGF), laminin, vascular endothelial growth factor (VEGF),and annexin V ligand based delivery systems (see U.S. Patent PublicationNo. 2005/0036984 to Harrison et al., which is hereby incorporated byreference in its entirety). In addition, a ligand for nucleophosmin,HSC70, BIP, Grp75, PDI, PDI ER60 precursor, HSP60, TCP-1ε, ERp29, HSP27,vimentin, α-internexin, cytokeratin 8, β-actin, γ-actin, β-tubulin,nm23-H1, valosin containing protein, tumor protein D52-like 2, ASF-2,hnRNPK, hnRNPC, 24.1D5 antigen, hnRNPA/B, Eukaryotic Elongation Factor1δ Isoform 2, AU-rich element RNA binding protein, Rad 23 homologue B,annexin I, prohibitin, ubiquilin 1, or thioredoxin peroxidase 4, whichare all surface markers for neoplastic cells (see U.S. PatentPublication No. 2007/0122414 to Georges et al., which is herebyincorporated by reference in its entirety), can also be used to targetdelivery of a macropinocytosis inhibitor of the invention to cancercells. Other cancer specific targeting peptides are disclosed by U.S.Patent Publication No. 2004/0102382 to Schughart et al., which is herebyincorporated by reference in its entirety.

To facilitate cellular uptake of the macropinocytosis inhibitor, theinhibitor can be further conjugated to a macropinocytosis targetingpeptide or ligand. Suitable macropinocytosis targeting peptides includearginine-rich synthetic or natural protein transduction domains.Exemplary macropinocytosis targeting peptides include, withoutlimitation RLRR (SEQ ID NO:1) and RRRQRRKKRG (HIV-TAT; SEQ ID NO:2). Themacropinocytosis targeting peptide can be conjugated directly to theinhibitor or can be combined with the cancer-specific targeting ligandto form a targeting ligand that directs cancer cell specific uptake ofthe inhibitor. An exemplary targeting peptide having dual specificity isdisclosed in Nishimura et al., “Combinatorial Targeting of theMacropinocytotic Pathway in Leukemia and Lymphoma Cells,” J. Biol. Chem.283(17):11752-62 (2008), which is hereby incorporated by reference inits entirety. This targeting peptide combines a lymph node homing motif(CAY) with an arginine-rich (RLRR) macropinocytosis motif to achieveselective uptake by leukemic/lymphoma cells. The resulting targetingpeptide has a sequence of CAYHRLRRC (SEQ ID NO:3).

An alternative approach for promoting the cellular uptake of amacropinocytosis inhibitor of the present invention is the use of a cellpenetrating peptide (CPP). CPPs translocate across the plasma membraneof eukaryotic cells by a seemingly energy-independent pathway and havebeen used successfully for intracellular delivery of macromolecules,including antibodies, peptides, proteins, and nucleic acids, withmolecular weights several times greater than their own. Several commonlyused CPPs, including polyarginines, transportant, protamine,maurocalcine, and M918, are suitable targeting moieties for use in thepresent invention and are well known in the art (see Stewart et al.,“Cell-Penetrating Peptides as Delivery Vehicles for Biology andMedicine,” Organic Biomolecular Chem 6:2242-2255 (2008), which is herebyincorporated by reference in its entirety). Additionally, methods ofmaking CPP are described in U.S. Patent Application Publication No.20080234183 to Hallbrink et al., which is hereby incorporated byreference in its entirety. The CPP can also be conjugated to acancer-specific targeting ligand to achieve dual-targeting specificity.

Another suitable moiety useful for enhancing the cellular uptake of themacropinocytosis inhibitor is an “importation competent” signal peptideas disclosed by U.S. Pat. No. 6,043,339 to Lin et al., which is herebyincorporated by reference in its entirety. An importation competentsignal peptide is generally about 10 to about 50 amino acid residues inlength, typically hydrophobic residues, that renders the inhibitorcapable of penetrating through the cell membrane from outside the cellto the interior of the cell. An exemplary importation competent signalpeptide includes the signal peptide from Kaposi fibroblast growth factor(see U.S. Pat. No. 6,043,339 to Lin et al., which is hereby incorporatedby reference in its entirety). Other suitable peptide sequences can beselected from the SIGPEP database (see von Heijne G., “SIGPEP: ASequence Database for Secretory Signal Peptides,” Protein Seq. DataAnal. 1(1):41-42 (1987), which is hereby incorporated by reference inits entirety). The importation competent signal peptide can further becoupled to the cancer-cell specific targeting ligand.

In accordance with the methods of the present invention, administering amacropinocytosis inhibitor to a subject can be carried out concurrentlywith other therapeutic approaches, i.e., the agent is administered aspart of a combination therapy. Accordingly, in one embodiment of theinvention, the agent is administered in combination with one or moreadditional cancer therapeutics such as, a chemotherapeutic, radiation(e.g., external beam radiation therapy or brachytherapy), ananti-angiogenic therapeutic, an anti-ras therapeutic, or an immuneenhancing therapeutic.

Suitable chemotherapeutic agents for combination therapies include,without limitation, alkylating agents (e.g., chlorambucil,cyclophophamide, CCNU, melphalan, procarbazine, thiotepa, BCNU, andbusulfan), antimetabolites (e.g., methotraxate, 6-mercaptopurine, and5-fluorouracil), anthracyclines (daunorubicin, doxorubicin, idarubicin,epirubicin, and mitoxantrone), antitumor antibiotics (e.g., bleomycin,monoclonal antibodies (e.g., Alemtuzumab, Bevacizumab, Cetuximab,Gemtuzumab, Ibritumomab, Panitumumab, Rituximab, Tositumomab, andTrastuxmab), platiniums (e.g., cisplatin and oxaliplatin) or plantalkaloids (e.g., topoisomerase inhibitors, vinca alkaloids, taxanes, andepipodophyllotoxins).

Anti-angiogenic therapeutics suitable for use in a combination therapyapproach with a macropinocytosis inhibitor of the invention include,without limitation a vascular endothelial growth factor (VEGF)inhibitor, basic fibroblast growth factor (bFGF) inhibitor, vascularendothelial growth factor receptor (VEGFR) antagonist, platelet-derivedgrowth factor receptor (PDGFR) antagonist, fibroblast growth factorreceptor (FGFR) antagonist, Angiopoietin receptor (Tie-2) antagonist,epidermal growth factor receptor (EGFR, ErbB) antagonist, or anycombination thereof. A number of suitable small molecule angiogenicinhibitors are known in the art or are under clinical development (see,e.g., Wu et al., “Anti-Angiogenic Therapeutic Drugs for the Treatment ofHuman Cancer,” J. Cancer Molecules 4(2):37-45 (2008), which is herebyincorporated by reference in its entirety). The angiogenic inhibitorsinclude, without limitation, Gefitinib (an ErbB inhibitor), Lapatinib (adual ErbB1/ErbB2 inhibitor), Erlotinib, Canertinib (a pan-ErbBinhibitor), Vatalanib (VEGF receptor inhibitor), Imatinib(multi-targeted inhibitor of Bcr-Abl, c-kit, and PDGF-R inhibitor),Sunitinib (multi-targeted inhibitor of VEGFR, PDGFR Kit, Flt3, Tet andCSF1R inhibitor), Sorafenib (multi-targeted inhibit of VEGFR and PDGFR),Pazopanib (a multi-targeted inhibitor of VEGFR-1, VEGFR-2, VEGFR-3,PDGF-α, PDGFR-β, and c-kit). Alternatively, the anti-vasculogenictherapeutic is a monoclonal antibody. Suitable antibody therapeuticsinclude, without limitation, Bevacizumab (VEGF antibody), IMC-1C11(VEGFR-2 antibody), mF4-31C1 (VEGFR-3 antibody), and Vitaxin (integrinα_(v)β₃ antibody).

Other anti-angiogenic as well as anti-stromal agents suitable for use ina combination therapy comprising a macropinocytosis inhibitor of thepresent invention are disclosed in Bissell et al., “Why Don't We GetMore Cancer? A Proposed Role of the Microenvironment in RestrainingCancer Progression,” Nat. Med. 17(3):320-329 (2011), which is herebyincorporated by reference in its entirety.

Suitable anti-ras therapeutic agents for use in combination with amacropinocytosis inhibitor of the present invention include, withoutlimitation, S-trans, transfarnesylthiosalicylic acid (FTS), a non-toxic,specific Ras antagonist (see Weisz et al., “A New Functional RasAntagonist Inhibits Human Pancreatic Tumor Growth in Nude Mice,”Oncogene 18(16):2579-2588 (1999), which is hereby incorporated byreference in its entirety), and the farnesyltransferase inhibitor,FTI-277, (see Bernhard et al., “The Farnesyltransferase InhibitorFTI-277 Radiosensitizes H-ras-transformed Rat Embryo Fibroblasts,”Cancer Research 56: 1727-1730 (1996), which is hereby incorporated byreference in its entirety).

In an alternative embodiment of the invention, the agent is administeredas a part of an adjuvant therapy regime. In particular, this involveschemotherapy, hormone therapy, radiation therapy, immunotherapy, or atargeted therapy together with an agent that inhibits macropinocytosisprior to and/or after surgery.

Pharmaceutical compositions containing macropinocytosis inhibitorssuitable for use in the methods of the present invention can include apharmaceutically acceptable carrier, one or more active agents, and asuitable delivery vehicle. Suitable delivery vehicles include, but arenot limited to viruses, bacteria, biodegradable microspheres,microparticles, nanoparticles, liposomes, collagen minipellets, andcochleates.

In one embodiment of the present invention, the delivery vehicle is aliposome delivery vehicle. Liposomes are vesicles comprised of one ormore concentrically ordered lipid bilayers which encapsulate an aqueousphase. A liposome which includes macropinocytosis inhibitor is contactedwith the target cancer cell under conditions effective for delivery ofthe inhibitory agent into the cancer cell. For administration to aprimary tumor site, the liposomal vesicles need not be targeted to thecancer cells per se. However, where the cancer cells to be treatedinclude metastatic cells and possible multiple secondary tumor sites,then it is desirable to administer liposomes that are targeted fordelivery to the cancer cells per se. The liposome delivery system can bemade to accumulate at a target organ, tissue, or cell via activetargeting (e.g., by incorporating an antibody or other ligand on thesurface of the liposomal vehicle). This can be achieved using antibodiesor ligands specific for an appropriate cancer cell marker as describedsupra.

Different types of liposomes can be prepared according to Bangham etal.,“Diffusion of Univalent Ions across the Lamellae of SwollenPhospholipids,” J. Mol. Biol. 13:238-252 (1965); U.S. Pat. No. 5,653,996to Hsu et al.; U.S. Pat. No. 5,643,599 to Lee et al.; U.S. Pat. No.5,885,613 to Holland et al.; U.S. Pat. No. 5,631,237 to Dzau et al.; andU.S. Pat. No. 5,059,421 to Loughrey et al., each of which is herebyincorporated by reference in its entirety.

These liposomes can be produced such that they contain, in addition tothe macropinocytosis inhibitor, other therapeutic agents, such asanti-inflammatory agents, chemotherapeutic agents, or immune-enhancingagents (e.g., IL-2 or interferon alpha or GM-CSF), which would also bereleased at the target site (e.g., Wolff et al., “The Use of MonoclonalAntiThy1-IgG1 for the Targeting of Liposomes to AKR-A Cells in vitro andin vivo,” Biochem. Biophys. Acta 802:259 (1984), which is herebyincorporated by reference in its entirety).

In another embodiment of the present invention, the delivery vehicle isa viral vector. Viral vectors are particularly suitable for the deliveryof inhibitory nucleic acid molecules, such as siRNA or shRNA molecules(e.g., when targeting ARF and/or Rho family of GTP-ases). Suitable genetherapy vectors include, without limitation, adenoviral vectors,adeno-associated viral vectors, retroviral vectors, lentiviral vectors,and herpes viral vectors.

Adenoviral viral vector delivery vehicles can be readily prepared andutilized as described in Berkner, “Development of Adenovirus Vectors forthe Expression of Heterologous Genes,” Biotechniques 6:616-627 (1988)and Rosenfeld et al., “Adenovirus-Mediated Transfer of a RecombinantAlpha 1-Antitrypsin Gene to the Lung Epithelium In Vivo,” Science252:431-434 (1991), WO 93/07283 to Curiel et al., WO 93/06223 toPerricaudet et al., and WO 93/07282 to Curiel et al., which are herebyincorporated by reference in their entirety. Adeno-associated viraldelivery vehicles can be constructed and used to deliver an inhibitorynucleic acid molecule of the present invention to cells as described inShi et al., “Therapeutic Expression of an Anti-Death Receptor-5Single-Chain Fixed Variable Region Prevents Tumor Growth in Mice,”Cancer Res. 66:11946-53 (2006); Fukuchi et al., “Anti-Aβ Single-ChainAntibody Delivery via Adeno-Associated Virus for Treatment ofAlzheimer's Disease,” Neurobiol. Dis. 23:502-511 (2006); Chatterjee etal., “Dual-Target Inhibition of HIV-1 In Vitro by Means of anAdeno-Associated Virus Antisense Vector,” Science 258:1485-1488 (1992);Ponnazhagan et al., “Suppression of Human Alpha-Globin Gene ExpressionMediated by the Recombinant Adeno-Associated Virus 2-Based AntisenseVectors,” J. Exp. Med. 179:733-738 (1994); and Zhou et al.,“Adeno-associated Virus 2-Mediated Transduction and ErythroidCell-Specific Expression of a Human Beta-Globin Gene,” Gene Ther.3:223-229 (1996), which are hereby incorporated by reference in theirentirety. In vivo use of these vehicles is described in Flotte et al.,“Stable in Vivo Expression of the Cystic Fibrosis TransmembraneConductance Regulator With an Adeno-Associated Virus Vector,” Proc.Nat'l. Acad. Sci. 90:10613-10617 (1993) and Kaplitt et al., “Long-TermGene Expression and Phenotypic Correction Using Adeno-Associated VirusVectors in the Mammalian Brain,” Nature Genet. 8:148-153 (1994), whichare hereby incorporated by reference in their entirety. Additional typesof adenovirus vectors are described in U.S. Pat. No. 6,057,155 toWickham et al.; U.S. Pat. No. 6,033,908 to Bout et al.; U.S. Pat. No.6,001,557 to Wilson et al.; U.S. Pat. No. 5,994,132 to Chamberlain etal.; U.S. Pat. No. 5,981,225 to Kochanek et al.; U.S. Pat. No. 5,885,808to Spooner et al.; and U.S. Pat. No. 5,871,727 to Curiel, which arehereby incorporated by reference in their entirety.

Retroviral vectors which have been modified to form infectivetransformation systems can also be used to deliver a nucleic acidmolecule to a target cell. One such type of retroviral vector isdisclosed in U.S. Pat. No. 5,849,586 to Kriegler et al., which is herebyincorporated by reference. Other nucleic acid delivery vehicles suitablefor use in the present invention include those disclosed in U.S. PatentPublication No. 20070219118 to Lu et al., which is hereby incorporatedby reference in its entirety.

Viral vectors are administered to a subject by, for example, intravenousinjection, local administration (U.S. Pat. No. 5,328,470 to Nabel etal., which is hereby incorporated by reference in its entirety) or bystereotactic injection (see e.g., Chen et al., “Gene Therapy for BrainTumors: Regression of Experimental Gliomas by Adenovirus Mediated GeneTransfer In Vivo,” Proc. Nat'l. Acad. Sci. USA 91:3054-3057 (1994),which is hereby incorporated by reference in its entirety). Thepharmaceutical preparation of the gene therapy vector can include thegene therapy vector in an acceptable diluent, or can comprise a slowrelease matrix in which the gene delivery vehicle is imbedded.

As an alternative to viral-vector delivery, nucleic acid moleculemacropinocytosis inhibitors (e.g., siRNA molecule) are encapsulated in alipid formulation to form a nucleic acid-lipid particle as described inSemple et al., “Rational Design of Cationic Lipids for siRNA Delivery,”Nature Biotech. 28:172-176 (2010) and WO2011/034798 to Bumcrot et al.,WO2009/111658 to Bumcrot et al., and WO2010/105209 to Bumcrot et al.,which are hereby incorporated by reference in their entirety.

In another embodiment of the present invention, the delivery vehicle isa nanoparticle. A variety of nanoparticle delivery vehicles are known inthe art and are suitable for delivery of a macropinocytosis inhibitor ofthe invention (see e.g., van Vlerken et al., “Multi-functional PolymericNanoparticles for Tumour-Targeted Drug Delivery,” Expert Opin. DrugDeliv. 3(2):205-216 (2006), which is hereby incorporated by reference inits entirety). Suitable nanoparticles include, without limitation,poly(beta-amino esters) (Sawicki et al., “Nanoparticle Delivery ofSuicide DNA for Epithelial Ovarian Cancer Cell Therapy,” Adv. Exp. Med.Biol. 622:209-219 (2008), which is hereby incorporated by reference inits entirety), polyethylenimine-alt-poly(ethylene glycol) copolymers(Park et al., “Degradable Polyethylenimine-alt-Poly(ethylene glycol)Copolymers As Novel Gene Carriers,” J. Control Release 105(3):367-80(2005) and Park et al., “Intratumoral Administration of Anti-KITENINshRNA-Loaded PEI-alt-PEG Nanoparticles Suppressed Colon CarcinomaEstablished Subcutaneously in Mice,” J Nanosci. Nanotechnology10(5):3280-3 (2010), which are hereby incorporated by reference in theirentirety), liposome-entrapped siRNA nanoparticles (Kenny et al., “NovelMultifunctional Nanoparticle Mediates siRNA Tumor Delivery,Visualization and Therapeutic Tumor Reduction In Vivo,” J. ControlRelease 149(2): 111-116 (2011), which is hereby incorporated byreference in its entirety). Other nanoparticle delivery vehiclessuitable for use in the present invention include microcapsule nanotubedevices disclosed in U.S. Patent Publication No. 2010/0215724 to Prakashet al., which is hereby incorporated by reference in its entirety.

In practicing the methods of the present invention, the administeringstep is carried out to achieve cancer cell specific inhibition ofmacropinocytosis, and such administration can be carried outsystemically or via direct or local administration, i.e., to a tumorsite. By way of example, suitable modes of systemic administrationinclude, without limitation, orally, topically, transdermally,parenterally, subcutaneously, intravenously, intramuscularly,intraperitoneally, by intranasal instillation, by intracavitary orintravesical instillation, intraocularly, intraarterially,intralesionally, or by application to mucous membranes. Suitable modesof local administration include, without limitation, catheterization,implantation, direct injection, dermal/transdermal application,stenting, ear/eye drops, or portal vein administration to relevanttissues, or any other local administration technique, method orprocedure, as is generally known in the art.

The agents of the present invention may be orally administered, forexample, with an inert diluent, or with an assimilable edible carrier,or it may be enclosed in hard or soft shell capsules, or it may becompressed into tablets, or they may be incorporated directly with thefood of the diet. Agents of the present invention may also beadministered in a time release manner incorporated within such devicesas time-release capsules or nanotubes. Such devices afford flexibilityrelative to time and dosage. For oral therapeutic administration, theagents of the present invention may be incorporated with excipients andused in the form of tablets, capsules, elixirs, suspensions, syrups, andthe like. Such compositions and preparations should contain at least0.1% of the agent, although lower concentrations may be effective andindeed optimal. The percentage of the agent in these compositions may,of course, be varied and may conveniently be between about 2% to about60% of the weight of the unit. The amount of an agent of the presentinvention in such therapeutically useful compositions is such that asuitable dosage will be obtained.

When the macropinocytosis inhibitors of the present invention areadministered parenterally, solutions or suspensions of the agent can beprepared in water suitably mixed with a surfactant such ashydroxypropylcellulose. Dispersions can also be prepared in glycerol,liquid polyethylene glycols, and mixtures thereof in oils. Illustrativeoils are those of petroleum, animal, vegetable, or synthetic origin, forexample, peanut oil, soybean oil, or mineral oil. In general, water,saline, aqueous dextrose and related sugar solution, and glycols, suchas propylene glycol or polyethylene glycol, are preferred liquidcarriers, particularly for injectable solutions. Under ordinaryconditions of storage and use, these preparations contain a preservativeto prevent the growth of microorganisms.

Pharmaceutical formulations suitable for injectable use include sterileaqueous solutions or dispersions and sterile powders for theextemporaneous preparation of sterile injectable solutions ordispersions. In all cases, the form must be sterile and must be fluid tothe extent that easy syringability exists. It must be stable under theconditions of manufacture and storage and must be preserved against thecontaminating action of microorganisms, such as bacteria and fungi. Thecarrier can be a solvent or dispersion medium containing, for example,water, ethanol, polyol (e.g., glycerol, propylene glycol, and liquidpolyethylene glycol), suitable mixtures thereof, and vegetable oils.

When it is desirable to deliver the agents of the present inventionsystemically, they may be formulated for parenteral administration byinjection, e.g., by bolus injection or continuous infusion. Formulationsfor injection may be presented in unit dosage form, e.g., in ampoules orin multi-dose containers, with an added preservative. The compositionsmay take such forms as suspensions, solutions or emulsions in oily oraqueous vehicles, and may contain formulatory agents such as suspending,stabilizing and/or dispersing agents.

Intraperitoneal or intrathecal administration of the agents of thepresent invention can also be achieved using infusion pump devices. Suchdevices allow continuous infusion of desired compounds avoiding multipleinjections and multiple manipulations.

Compositions containing macropinocytosis inhibitors may also beformulated as a depot preparation. Such long acting formulations may beformulated with suitable polymeric or hydrophobic materials (for exampleas an emulsion in an acceptable oil) or ion exchange resins, or assparingly soluble derivatives, for example, as a sparingly soluble salt

Effective doses of the compositions of the present invention, for thetreatment of cancer vary depending upon many different factors,including type and stage of cancer, means of administration, targetsite, physiological state of the patient, other medications or therapiesadministered, and physical state of the patient relative to othermedical complications. Treatment dosages need to be titrated to optimizesafety and efficacy.

Another aspect of the present invention is directed to a method ofdiagnosing cancer in a subject. This method involves administering tothe cells of a subject a macropinocytosis marker and detecting thepresence of the macropinocytosis marker in cells of the subject. Themethod further involves comparing the amount of macropinocytosis markerin cells of the subject to the amount of macropinocytosis marker innon-cancer cells and making a diagnosis of cancer in the subject basedon this comparison.

In accordance with this aspect of the invention, an increase in theamount of macropinocytosis marker in cells of the subject compared tonon-cancer cells indicates the subject has cancer. In a preferredembodiment of the present invention, a subject diagnosed with havingcancer is treated with a macropinocytosis inhibitor in accordance withthe methods of the present invention.

This diagnostic method of the invention can be carried out using cellsobtained from the subject ex vivo or by direct administration of thelabeled macropinocytosis marker to the subject in vivo as describedbelow.

In accordance with this aspect of the present invention, an oncogenemediated cancer can be diagnosed. For example, any cancer involving anoncogenic ras, v-src, or oncogenic EGFR can be diagnosed. Suitablecancers for diagnosis include, without limitation, pancreatic cancer,lung cancer, colorectal cancer, thyroid cancer, liver cancer, bladdercancer, and leukemia.

Suitable macropinocytosis markers are biomolecules that are taken up viamacropinocytosis, such as dextran, arginine rich peptides, peptides, andproteins (e.g., albumin). The macropinocytosis marker can furthercomprise a macropinocytosis targeting motif as described supra (e.g., anarginine-rich amino acid sequence). The macropinocytosis marker can belabeled with a radioisotope, fluorescent label, bioluminescent label orother label that is suitable for ex vivo and in vivo detection methods.

In one embodiment, the macropinocytosis inhibitor is radiolabeled.Suitable radioactive labels include ¹²⁵I, ¹³¹I, ¹¹¹In, or ⁹⁹TC. Methodsof radiolabeling targeting components, are known in the art anddescribed in U.S. Pat. No. 5,514,363 to Shochat et al., which is herebyincorporated by reference in its entirety. Radioactivity is detected andquantified using a scintillation counter or autoradiography.

In another embodiment of the invention, the macropinocytosis marker islabeled with a fluorescent label. Exemplary fluorescent labels includechelates (europium chelates), fluorescein and its derivatives, rhodamineand its derivatives, dansyl, Lissamine, phycoerythrin and Texas Red. Thefluorescent labels can be conjugated to the macropinocytosis markerusing the techniques disclosed in CURRENT PROTOCOLS IN IMMUNOLOGY(Coligen et al. eds., 1991), which is hereby incorporated by referencein its entirety. Fluorescence can be detected and quantified using afluorometer.

Exemplary bioluminescent labels include, without limitation, obelin(Matveev et al., “Genetically Engineered Obelin as a BioluminescentLabel in an Assay for a Peptide,” Anal. Biochem. 270(1):69-74 (1999),which is hereby incorporated by reference in its entirety), liposomalaequorin (Ho et al., “Application of a Liposomal Bioluminescent Label inthe Development of a Flow Injection Immunoanalytical System,” Anal.Chem. 77(11): 3431-36 (2005), which is hereby incorporated by referencein its entirety), and Aqualite® (Smith et al., “Aqualite, aBioluminescent Label for Immunoassay and Nucleic Acid Detection:Quantitative Analyses at the Attomol Level,” Proc. SPIE 2680:156-66(1996), which is hereby incorporated by reference in its entirety).

As mentioned above, the diagnostic method of the present invention canbe carried out by direct administration of the labeled marker to asubject in vivo. This involves administering (for example, parenterally,subcutaneously, or intraperitoneally) the labeled macropinocytosismarker to the subject, permitting the labeled molecule to be taken upvia the macropinocytotic mechanism, allowing clearance of labeled markernot taken up by macropinocytosis, and detecting the amount or level oflabeled marker in the subject after a suitable time interval followingthe administration. The detected amount is then compared to the level oflabeled marker taken up by non-cancer cells. This comparison can be madeto the uptake of the marker by the same cells of the subject assessed atan early timepoint (i.e., a previous test) or to cells of the subjectknown to be healthy, cancer free cells.

The background level of macropinocytosis in a subject can be determinedby various methods including, comparing the amount of labeled moleculedetected to a standard value previously determined for a particularsystem. The size of the subject and the imaging system used willdetermine the quantity of imaging moiety needed to produce diagnosticimages.

In the case of a radioisotope moiety, for a human subject, the quantityof radioactivity injected will normally range from about 5 to 20millicuries of ⁹⁹Tc. The labeled marker will then preferentiallyaccumulate within cells having enhanced macropinocytosis. In vivoimaging is described in Burchiel et al., Immunopharmacokinetics ofRadiolabeled Antibodies and Their Fragments, IN TUMOR IMAGING: THERADIOCHEMICAL DETECTION OF CANCER (Burchiel et al. eds., 1982), which ishereby incorporated by reference in its entirety.

Depending on several variables, including the type of label used and themode of administration, the time interval following the administrationfor permitting the labeled molecule to preferentially concentrate atsites in the subject and for unbound labeled molecule to be cleared tobackground level is 6 to 48 hours, 6 to 24 hours, or 6 to 12 hours. Inanother embodiment the time interval following administration is 5 to 20days or 5 to 10 days.

The presence of the labeled molecule can be detected in the patientusing methods known in the art for in vivo scanning and imaging of thebody. These methods depend upon the type of label used. Skilled artisanswill be able to determine the appropriate method for detecting aparticular label. Methods and devices that may be used in the diagnosticmethods of the invention include, but are not limited to, computedtomography (CT), whole body scan such as position emission tomography(PET), magnetic resonance imaging (MRI), and sonography. In oneembodiment, the macropinocytosis marker is labeled with a radioisotopeand is detected in the patient using a radiation responsive surgicalinstrument (U.S. Pat. No. 5,441,050 to Thurston et al., which is herebyincorporated by reference in its entirety). In another embodiment, themacropinocytosis marker is labeled with a fluorescent compound and isdetected in the patient using a fluorescence responsive scanninginstrument. In another embodiment, the macropinocytosis marker islabeled with a positron emitting metal and is detected in the patientusing positron emission-tomography. In yet another embodiment, themacropinocytosis marker is labeled with a paramagnetic label and isdetected in a patient using magnetic resonance imaging (MRI).

In one embodiment, monitoring the status of the cancer can be carriedout by repeating the method for diagnosing the presence of cancer, forexample, one month after initial diagnosis, six months after initialdiagnosis, one year after initial diagnosis, etc. Monitoring the statusof the cancer is particularly suitable when determining theresponsiveness of a tumor to a particular course of therapeutictreatment.

Another aspect of the present invention is directed to a high-throughputmethod of identifying a cancer therapeutic. This method involvesproviding a population of cancer cells having enhanced macropinocytosisand providing a macropinocytosis marker. The method further involvescontacting the population of cells with a candidate compound underconditions effective for the candidate compound to inhibitmacropinocytosis and detecting and comparing the macropinocytotic uptakeof the macropinocytosis marker in the presence and in the absence of thecandidate compound. A decrease in marker uptake in the presence of thecandidate compound compared to in the absence of the candidate compoundidentifies a cancer therapeutic. A detailed description of this aspectof the invention is described in Example 6 below.

In accordance with this aspect of the invention, the population of cellshaving enhanced macropinocytosis comprise an oncogene. In one embodimentof the invention, the population of cells comprise an oncogenic ras,src, or EGFR gene.

Suitable macropinocytosis markers and labels for the markers aredescribed supra.

EXAMPLES

The following examples are provided to illustrate embodiments of thepresent invention but they are by no means intended to limit its scope

Example 1—Macropinocytosis in Oncogenic Ras Cells

The detection of stimulated fluid-phase macropinocytosis in human cellscan be monitored using conventional fluorescent microscopy via theuptake of fluorescent 70 kDa dextran (FITC-dextran), a marker ofmacropinocytosis. In cells expressing an oncogenic form of Ras(Ras^(V12)), uptake of fluorescent dextran is apparent within severalminutes and is dramatically increased compared to control cells (FIG.1A). For the quantification of macropinocytosis, an intensity-basedread-out assay that is described herein was used. This involvesmonitoring the uptake of FITC-dextran in HeLa cells that have beengenetically modified to conditionally express H-Ras^(V12) (Sparmann etal., “Ras-Induced Iinterleukin-8 Expression Plays a Critical Role inTumor Growth and Angiogenesis,” Cancer Cell 6(5):447-58 (2004), which ishereby incorporated by reference in its entirety). Quantification ofmacropinosomes in oncogenic Ras^(V12)-expressing cells indicates anapproximate 30-fold increase when compared to uninduced control cells(FIG. 1B).

As an extension to these findings, macropinocytosis in murineimmortalized fibroblast cells was analyzed. Untransformed NIH3T3 cellsdisplay low levels of macropinocytosis, compared toRas^(V12)-transformed cells (FIG. 2A). Using an amended protocol,fluid-phase uptake in these cells was quantified. K-Ras^(V12)-expressingcells have a 3-4 fold increase in macropinocytosis (FIG. 2B).

Example 2—Macropinocytosis in Oncogenic Cancer Cells

It was postulated that cancer cells harboring oncogenic Ras mutationswould display higher levels of macropinocytosis compared to cancer cellshaving a non-mutant Ras. For pancreatic cancer cells, macropinocytosiswas analyzed in MIA-Paca-2 cells, which are homozygous for the oncogenicK-Ras^(G12C) allele (Lopez-Crapez et al., “Rapid and Large-Scale Methodto Detect K-Ras Gene Mutations in Tumor Samples,” Clin. Chem. 43(6 Pt1):936-42 (1997) and Pretlow et al., “K-Ras Mutations in PutativePreneoplastic Lesions in Human Colon,” J. Natl. Cancer Inst.85(24):2004-7 (1993), which are hereby incorporated by reference intheir entirety) and BxPc-3 cells that only express wild-type K-Ras (Aokiet al., “Liposome-Mediated in vivo Gene Transfer of Antisense K-RasConstruct Inhibits Pancreatic Tumor Dissemination in the MurinePeritoneal Cavity,” Cancer Res. 55(17):3810-6 (1995), which is herebyincorporated by reference in its entirety). As a bladder model, uptakein T24 and 5637 cells was analyzed. T24 cells are homozygous for theoncogenic H-Ras^(V12C) allele and 5637 cells only express wild-typeH-Ras. Macropinosomes were visualized based on their ability toincorporate from the extracellular medium a tetramethylrhodamine-labeled70 kDa dextran (TMR-dextran), an established marker of macropinocytosis(Kerr et al., “Defining Macropinocytosis,” Traffic 10(4):364-71 (2009),which is hereby incorporated by reference in its entirety). The dataindicates that macropinocytosis in MIA-Paca-2 (FIGS. 3D and 3E) and T24cells (FIG. 3B) is appreciably higher compared to wild-type Ras cells(FIGS. 3A and 3C). TMR-dextran labeling in MIA-Paca-2 and T24 cellsreflects uptake via macropinocytosis because it was inhibited bytreatment with the amiloride analog EIPA, a macropinocytosis inhibitorthat functions by inhibiting Na⁺/H⁺ exchange (Ivanov, “PharmacologicalInhibition of Endocytic Pathways: Is it Specific Enough to be Useful?”Methods Mol. Biol. 440:15-33 (2008), which is hereby incorporated byreference in its entirety). These results suggest that Ras-transformedcancer cells of display stimulated macropinocytosis.

To determine the extent of stimulated macropinocytosis in a setting ofendogenous tumors, p48-Cre;LSL-KRas^(G12D) mice were utilized. Thesemice gradually develop pancreatic intraepithelial neoplasias (PanINs)that infrequently progress to invasive pancreatic ductal adenocarcinoma(PDA) (Hingorani et al., “Preinvasive and Invasive Ductal PancreaticCancer and its Early Detection in the Mouse,” Cancer Cell 4(6): 437-50(2003), which is hereby incorporated by reference in its entirety). Ininitial studies, these mice were injected at two months of age with 2 mgFITC-dextran, and pancreata were harvested two hours post-injection. Asa control, pancreatic tissue from wild-type mice was also analyzed.Frozen sections from sectioned pancreata were analyzed using standardmicroscopic techniques and macropinocytosis-positive cells wereidentified by the visualization of FITC-positive puncta. There was anincrease in the number of macropinocytosis-positive cells in pancreatictissue expressing oncogenic K-Ras, compared to wild-type. To control fororgan specificity, tissue originating from the liver, duodenum, andcolon was analyzed and no appreciable uptake of the macropinocytosismarker in either wild-type or mutant tissue was observed. The identityof the cells using immunostaining various cell markers indicates thatthe macropinocytosis-positive cells in this particular cancer model areimmune in origin as indicated by their CD45 positivity (FIGS. 4C-4D).

This dramatic display of macropinocytosis has clear diagnosticimplications as described supra. Early pancreatic lesions can bedetected by measuring the extent of macropinocytosis positivity withinan organ. The number of macropinocytosis-positive immune cellscorresponds to the progression of PanIN lesions as their frequency ishigher in older animals (ranging from 1-7 months) that exhibit anage-dependent increase in the number and stage of lesions documented(Deramaudt et al., “Mutant KRAS in the Initiation of Pancreatic Cancer,”Biochim. Biophys. Acta. 1756(2):97-101 (2005), which is herebyincorporated by reference in its entirety).

Example 3—Macropinocytosis in Heterotopic Xenograft Tumors Derived fromHuman MIA-PaCa-2 Pancreatic Cancer Cells

To establish the in vivo prevalence of macropinocytosis in pancreaticcancer, an experimental xenograft mouse model was employed. For thexenograft model, 1×10⁶ pancreatic cancer cells (MIA-PaCa-2) wereinjected subcutaneously into the flanks of nude mice (FIG. 5A).Macropinocytosis by the tumor cells was analyzed at 3 weekspost-injection, when the tumors attained an average volume of 300-500mm³. To detect macropinocytosis in tumor cells, mice were intratumorallyinjected with a fluorescently-labeled fluid-phase marker (FITC-dextran)at 2 mg/g. The presence of macropinocytosis-positive cells within thetumors was assessed by the microscopic visualization of FITC-positivepuncta in frozen sections (FIGS. 5C and 5E; cell nuclear localization isshown using DAPI in FIGS. 5B and 5E). To distinguish betweentransplanted and host immune/stromal cells, the sections werecounterstained with an epithelial-specific anti-cytokeratin antibody(FIGS. 5D and 5E).

Example 4—Protein Uptake in Oncogenic Ras Cells

When added to the growth medium, fluorescently-labeled bovine serumalbumin (FITC-BSA) was incorporated into vesicular compartments inoncogenic Ras^(V12)-expressing HeLa cells (FIG. 6A), MIA-Paca-2, and T24cells. This internalization process was inhibited by EIPA, suggestingthat cancer cells harboring Ras mutations can internalize extracellularprotein via macropinocytosis. Quantification of FITC-BSA uptake wasperformed utilizing an amended form of the high-throughput protocoldescribed herein (FIG. 6B). Using colocalization experiments, it wasobserved that FITC-BSA is internalized with a macropinocytosis marker,dextran (FIG. 7A-7C). To be utilized as a nutrient source, the proteincontents of Ras-stimulated macropinosomes must be delivered to adegradative compartment, such as the lysosome. The fate of themacropinosomes was followed via pulse chase experiments and their fusionwith lysosomes was monitored by co-staining with lysosomal markers (i.e.Lysotracker). Cells were pulsed with TMR-dextran and incubated withTMR-dextran-free media for varying intervals. At the end of theincubation period, cells were stained with a lysosomal marker andvisualized by fluorescent microscopy. FIG. 9 shows that macropinsomecontents are destined for an acidic lysosomal compartment.

Albumin degradation was measured via a pulse-chase experiment consistingof incubating oncogenic Ras^(V12)-expressing HeLa cells with BSA andsubsequently chasing with BSA-free media. The presence of internalizedBSA was measured by immunostaining the cells with an anti-BSA antibodyand a fluorescent secondary antibody (FIG. 10A). Subsequently, theintensity of the fluorescent signal that was incorporated into vesicularspots was quantified using automated spot detection (FIG. 10B).

To demonstrate that glutamine and glutamate production results from thedegradation of albumin, K-Ras transformed NIH 3T3 cells were incubatedwith either low (0.4%) or physiological (2%) concentrations of albuminfor 24 hours. Cells were harvested and the intracellular glutamine (FIG.11B) and glutamate (FIG. 11B) concentration was determined using theEnzyChrom Glutamine Assay Kit (BioAssay Systems).

Example 5—Survival and Growth of Oncogenic Ras Expressing Cells in LowGlutamine Conditions

Glutamine, the most abundant amino acid in mammals, is required fortumor cell proliferation and is critical to tumor cell bioenergetics andmacromolecular biosynthesis (DeBerardinis et al., “The Biology ofCancer: Metabolic Reprogramming Fuels Cell Growth and Proliferation,”Cell Metab. 7(1):11-20 (2008), which is hereby incorporated by referencein its entirety). Under physiological conditions, glutamine is suppliedby interstitial fluids and blood plasma and is internalized by cells viavarious glutamine transport systems (McGivan et al., “The Transport ofGlutamine into Mammalian Cells,” Front Biosci. 12:874-82 (2007), whichis hereby incorporated by reference in its entirety). In tumor cells,however, the rate of glutamine consumption is markedly increased leadingto the depletion of free glutamine (Medina “Glutamine and cancer,” J.Nutr. 131(9 Suppl):2539S-42S (2001), which is hereby incorporated byreference in its entirety). Therefore, glutamine availability to thetumor may become limiting, invoking the need for alternative glutaminesources. Physiological fluids are composed of up to 70% protein, most ofwhich is serum albumin, a potentially rich source of amino acids fortumor cells (Stehle et al., “Plasma Protein (Albumin) Catabolism by theTumor Itself—Implications for Tumor Metabolism and the Genesis ofCachexia,” Crit. Rev. Oncol. Hematol. 26(2)77-100 (1997), which ishereby incorporated by reference in its entirety). The data hereinindicate that the internalization of extracellular serum albumin viamacropinocytosis, an endocytic mechanism of fluid-phase uptake, canserve to augment the glutamine supply (FIGS. 11A-11B) and that thismechanism contributes to pancreatic cancer cell growth and survival.

If albumin internalization via Ras-stimulated macropinocytosis serves toaugment the glutamine supply, then this process should confer a survivaland growth advantage under conditions where free glutamine is limiting.To test this prediction, the survival of oncogenic Ras^(V12)-expressingHeLa cells was tested. Under glutamine starvation (0 mM) conditions andin the presence of low albumin concentrations (0.2%), theRas^(V12)-expressing cells exhibit a survival advantage (FIG. 12B). Itwas hypothesized that this was due to albumin-derived amino acids thatwere augmenting the intracellular glutamine supply. It was determinedthat Ras^(V12)-survival was enhanced at higher concentrations ofextracellular albumin (up to 2%; FIG. 13) and that this survivalenhancement was suppressed by EIPA, a macropinocytosis inhibitor (FIGS.14A-14B).

These findings were extended by analyzing glutamine-deprivation andsurvival in K-Ras-transformed NIH 3T3 cells. K-Ras^(V12)-expressingNIH3T3 cells are exquisitely sensitive to glutamine deprivation and theglutamine addiction displayed by these cells is selectively andpartially rescued by increasing the concentration of extracellularalbumin (FIG. 15). These findings were corroborated by the analyses incancer cell lines harboring Ras-mutations, which yielded similar results(FIG. 16).

Next, whether the proliferative defect of cancer cells in low glutamine(0.2 mM) can be rescued by the supplementation of the growth medium withphysiological concentrations of serum albumin (2-4%) was examined. Thiswas determined to be the case using K-Ras^(V12)-expressing NIH3T3 cells(FIG. 18). Additionally this observation was noted in T24 cells, whichharbor oncogenic H-Ras, but not in 5637 cells, which only expresswild-type H-Ras (FIGS. 19A-19B).

Example 6—Albumin Supplementation and Cell Growth are Connected toGlutamine Metabolism

Glutamine is a major nutrient for many proliferating cells and israpidly metabolized to glutamate, then α-ketoglutarate to enter centralcarbon metabolism. To test whether the favorable effects of albuminsupplementation on cell growth were related to glutamine metabolism, theintracellular concentrations of glutamate and α-ketoglutarate in cellsgrown either in the absence or presence of albumin was measured. NIH 3T3[K-Ras^(G12V)] cells were cultured for 24 hours in complete media (CM)supplemented to physiological concentrations of albumin (2 g/100 mL,2%). As a control, NIH 3T3 [K-Ras^(G12V)] cells were also cultured in CMalone, which contains minimal levels of albumin (˜0.2%). Cells werelysed and metabolite levels were determined from deproteinized celllysates. The addition of albumin to the media led to significantincreases in intracellular concentrations of both glutamate andα-ketoglutarate (FIG. 20A). These albumin-dependent increases in bothglutamate and α-ketoglutarate were blocked by EIPA treatment (FIG. 20A),suggesting that macropinocytic uptake of albumin can promoteaccumulation of glutamine catabolic intermediates in oncogenicRas-transformed cells. Consistent with this idea, the anti-proliferativeresponse to EIPA observed in the presence of physiological albumin wasrescued by increased levels of glutamine and by exogenousα-ketoglutarate (FIG. 20B). Together, these data suggest that themacropinocytic uptake of albumin facilitates proliferation under lowglutamine conditions due to the intracellular production of glutamineand potentially other amino acids.

In order for the macropinocytosis of albumin to constitute a mechanismof amino acid supply, the internalized albumin would have to be destinedfor proteolytic degradation. To detect intracellular degradation ofalbumin, a highly self-quenched BODIPY dye conjugated form of BSA(DQ-BSA) that only emits a bright fluorescent signal upon proteolyticdigestion was utilized. Dual labeling of NIH 3T3 [K-Ras^(G12V)] cellswith DQ-BSA and TMR-dextran was used to determine the macropinocyticorigin of the degradative compartment. In cells that were immediatelyfixed following a 30 minute incubation with DQ-BSA and TMR-dextran(T=0), there was no appreciable DQ-BSA fluorescence detected inmacropinosomes (FIG. 20C). However, in cells that were incubated for 30minutes and subsequently chased for 1 hour in media free of both DQ-BSAand TMR-dextran, a significant level of DQ-BSA fluorescence was detectedin TMR-positive macropinosomes (FIG. 20C). DQ-BSA fluorescence was alsodetected within macropinosomes after a 1 hour chase in MIA PaCa-2 andT24 cells, indicating that these trafficking events were also occurringin cancer cells harboring endogenous oncogenic Ras mutations. These datademonstrate that oncogenic Ras-expressing cells can harnessmacropinocytosis for the internalization and degradation ofextracellular albumin, and raise the possibility that albumin-derivedamino acids may accumulate intracellularly.

Example 7—A High Throughput-Compatible Macropinocytosis Assay

To analyze and quantify Ras-stimulated macropinocytosis, a high contentscreening (HCS)-compatible platform designed for rapid spot analysis wasdesired. One such platform is the Arrayscan HCS Reader (Cellomics) inconjunction with the Spot Detector BioApplication (Cellomics), which isdesigned to provide fluorescent- and image-based generic spot analysisfor multiple biological applications. As a model cell-based system, aHeLa Tet-Off (HTO) cell line (Clontech) stably transfected with atetracycline-repressible transgene encoding an oncogenic form ofhemagglutinin (HA)-tagged H-Ras (H-Ras^(V12)) was used. In brief, 2000cells per well were plated in 384-well plate format in a total volume of50 μL. To induce expression of H-Ras^(V12), cells were plated in medialacking tetracycline, while control cells were plated in 50 ng/mLtetracycline. Twenty-four hours after plating, cells were washed onetime with PBS and incubated for 24 hours in serum-free media (eithercontaining 50 ng/mL tetracycline or tertacycline-free). Themacropinocytosis assay consisted of the addition of a 70 kDatetramethylrhodamine-labelled dextran (TMR-dextran, Invitrogen) to themedia. After a 30 minute incubation period, cells were washed twice withcold PBS, fixed and DAPI-stained.

Macropinosomes were analyzed on a cell-to-cell basis using multichannelanalysis on the Arrayscan HCS Reader (FIG. 21A). Primary objects (cells)were located by the DAPI stained nuclei on Channel 1. A circular spotidentification target region (or mask) was then applied for each objecton Channel 2, and spots were detected based on their fluorescentintensity, size, and shape. As expected, spot identification wassignificantly higher in cells expressing oncogenic H-Ras (FIG. 21A,compare the right-most images with HeLa [vector] only shown in the topimage and HeLa[H-Ras^(V12)] shown in the bottom image, spotidentification is shown in red). To quantify this, the output featureselected for Channel 2 was Spot Count Per Object, which is effectively ameasure of total number amount of fluorescent extracellular fluidinternalized per cell in a given incubation time. H-Ras^(V12)-expressingcells have a 8- to 9-fold increase in the levels of fluid-phase uptakecompared to cells assayed in tetracycline (FIG. 21B).

One of the advantages of using the Tet-Off repression system is thatlevels of the transgene of interest can be finely controlled via theconcentration of tetracycline supplemented to the medium. Withdecreasing levels of tetracycline, levels of H-Ras^(V12) are increased(FIG. 12A) and resulting in a concomitant increase in fluid-phase uptake(FIG. 1B). Varying tetracycline concentrations did not affectmacropinocytosis in the parental HTO cell line, demonstrating that thestimulation of macropinocytosis is directly correlated to levels ofH-Ras^(V12) expression.

An advantage to using the Spot Detector BioApplication is that inaddition to well-level features, the software also provides field-levelresults. Field-level data can be useful in high-throughput analyses todetermine the intra-well variation. Within a given concentration oftetracycline, the spot total intensity per object did not vary greatly,however, cells grown in tetracycline-free media had the greatestdifference compared to control cells.

To determine the feasibility of using this high throughput assay toidentify novel chemical inhibitors of Ras-stimulated macropinocytosis,the effects of known macropinocytosis inhibitors were evaluated. Theactivation of phosphoinositide 3-kinases (PI3Ks) is required for thestimulation of macropinocytosis. PI3Ks are potently inhibited by2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4 (LY294002), which exertsits effects by selectively targeting the ATP-binding site of the kinase.The effects of LY294002 on Ras-stimulated macropinocytosis were assessedusing this HT assay.

HeLa cells expressing HA-H-Ras^(V12) were plated in 384-well format at2500 cells per well. After 24 hours, cells were washed with PBS andgrowth media was replaced with serum free media and incubated for 24hours. For the inhibition assay, cells were pre-incubated with variousconcentrations of LY294002 in serum-free media for 30 minutes. This wasfollowed by the addition of TMR-dextran for 30 minutes and plates weresubsequently processed as described earlier. High content analysisrevealed a dose-response relationship with maximal inhibition ofmacropinocytosis occurring at 100 μM LY294002 (FIG. 22A).

Macropinocytosis is also potently inhibited by Na⁺/H⁺ exchangerinhibitors such as amiloride and its analogs. Amiloride likely exertsits effects on macropinoctyosis by lowering the submembranous pH andinterfering with the activation of GTPases that promote actinremodeling. EIPA, an amiloride analog, selectively inhibits the Na⁺/H⁺exchanger, is soluble in cell culture media, and exerts its effects atmuch lower concentrations (50-100 μM) compared to amiloride (1-5 mM).Therefore, EIPA treatment was used to further validate the highthroughput assay.

The inhibition assay using EIPA was similar to that described forLY294002. Treatment with EIPA resulted in a dose-response relationshipwith maximal inhibition of macropinocytosis occurring at 100 μM (FIG.22B)

To explore the flexibility of the high-throughput compatiblemacropinocytosis assay, the HeLa-based Spot Detector BioApplicationparameters were amended to quantify macropinocytosis inK-Ras^(V12)-expressing NIH3T3 cells. To do this, object identificationparameters were altered to accommodate larger nuclei and the spotidentification target region was adjusted accordingly.

Untransformed NIH3T3 cells display low levels of macropinocytosis,compared to K-Ras^(V12)-transformed cells. Using this amended protocol,it was possible to quantify fluid-phase uptake in these cells anddetermine that K-Ras^(V12)-expressing cells have a 3-4 fold increase inmacropinocytosis (FIGS. 2A-2B). To examine the effects ofmacropinocytosis inhibitors, K-Ras^(V12)-transformed NIH3T3 cells weretreated with increasing concentrations of LY294002 or EIPA.Quantification of macropinocytosis via the high-throughput assayrevealed a dose-response relationship for both inhibitors. Altogether,these data indicate that the high-throughput-compatible macropinocytosisassay of the present invention can be amended to accommodate other celltypes, and that known macropinocytosis inhibitors have a measurableeffect on both H-Ras- and K-Ras-stimulated macropinocytosis.

Although the invention has been described in detail for the purpose ofillustration, it is understood that such detail is solely for thatpurpose, and variations can be made therein by those skilled in the artwithout departing from the spirit and scope of the invention which isdefined in the following claims.

What is claimed:
 1. A method comprising: selecting a subject havingcancer; administering to the selected subject an agent selected from thegroup consisting of dextran, albumin, poly(beta-amino ester)nanoparticles, polyethylenimine-alt-poly(ethylene glycol) copolymernanoparticles, and lipid nanoparticles; detecting the presence of theagent in cells of the subject; and quantifying the presence of the agentin cancerous cells and non-cancerous cells of the subject.
 2. The methodaccording to claim 1, wherein the selected subject has an oncogenemediated cancer.
 3. The method according to claim 2, wherein theoncogene mediated cancer is selected from the group consisting ofras-mediated cancer, src-mediated cancer, and EGFR-mediated cancer.
 4. Amethod according to claim 1, wherein the selected subject has a cancerselected from the group consisting of pancreatic cancer, lung cancer,colorectal cancer, thyroid cancer, liver cancer, and leukemia.
 5. Themethod according to claim 1, wherein the agent is labeled with afluorescent label, a bioluminescent label, or a radioisotope.
 6. Themethod according to claim 1, further comprising: administering achemotherapeutic agent to the subject based on said quantifying.
 7. Themethod according to claim 1, further comprising: administering amacropinocytosis inhibitor to the subject based on said quantifying,wherein said macropinocytosis inhibitor is selected from the groupconsisting of wortmannin, LY294002, amiloride, and an analogue ofamiloride.